Spark Plugs and Computer

I just got done putting in some new NGK plugs into my '95 Protege 1.5 . It had been about two years since last doing it. Looking at the gap on the old plugs, they were at .045" or out of spec by .002". The new ones were gapped at .040", just above the .039" minimum gap allowed. When I started up the car it initially ran rough and the check engine light came on. Also, the idle was quite low after warming up. Realizing that my young son had been in the car using all the accessories for the last several days, I guessed that that battery had been drained and was not fully charged when I started the car. Also, I did not disconnect the battery when doing the plug change so the computer was not reset.

So had the computer remembered the old gap at startup and this caused the rough start or just the drained battery? One thing I realize about the Protege is that it seems to have an undersized charging system compared to other larger vehicles.

I subsequently disconnected the battery terminal and reset the computer and also drove the car for awhile to fully charge the battery and everything is running good again.